regionUpset: regionUpset

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

regionUpset

Description

A wrapper around upset for comparing multiple sets of genomic ranges.

Usage

regionUpset(
  x,
  reference = c("reduce", "disjoin"),
  returnList = FALSE,
  ignore.strand = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  ...
)

Arguments

x	A named list of genomic ranges (or paths to bed files)
reference	The method for creating the reference windows ('reduce' or 'disjoin'). Alternatively, a 'GRanges' object of reference windows.
returnList	Logical; whether to return the list instead of plotting.
ignore.strand	Logical; whether to ignore strands when computing overlaps (default FALSE). Strand information is ignored if either of the compared sets of regions is unstranded.
maxgap	Maximum gap between regions to count as an overlap (see findOverlaps-methods).
minoverlap	Minimum overlap to count as a match (see findOverlaps-methods).
...	Further plotting arguments passed to upset.

Value

A plot

Examples

# random list of GRanges:
grl <- lapply(c(A=10,B=20,C=30), FUN=function(x){
  GRanges("seq1", IRanges(runif(x,1,1000), width=20))
})
regionUpset(grl)

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.